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Adding argument force.first.aa.to.Met (Dr. Haruo Suzuki suggestion) #8

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Dec 13, 2023
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Adding argument force.first.aa.to.Met (Dr. Haruo Suzuki suggestion) #8

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2 changes: 1 addition & 1 deletion DESCRIPTION
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@@ -1,6 +1,6 @@
Package: seqinr
Title: Biological Sequences Retrieval and Analysis
Version: 4.2-36
Version: 4.2-37
Depends: R (>= 2.10.0)
Imports: ade4,segmented
Authors@R: c(person("Delphine", "Charif", role = "aut"),
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32 changes: 20 additions & 12 deletions R/getTrans.R
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Expand Up @@ -2,34 +2,42 @@
# To translate sequences:
#

getTrans <- function(object, sens = "F", NAstring = "X", ambiguous = FALSE, ...)
getTrans <- function(object, sens = "F", NAstring = "X", ambiguous = FALSE, force.first.aa.to.Met = FALSE, ...)
UseMethod("getTrans")

getTrans.default <- function(object, sens = "F", NAstring = "X", ambiguous = FALSE, ...)
getTrans.default <- function(object, sens = "F", NAstring = "X", ambiguous = FALSE, force.first.aa.to.Met = FALSE, ...)
stop(paste("no getTrans method for objects of class:", class(object)))

getTrans.list <- function(object, sens = "F", NAstring = "X", ambiguous = FALSE, ...)
getTrans.list <- function(object, sens = "F", NAstring = "X", ambiguous = FALSE, force.first.aa.to.Met = FALSE, ...)
lapply(seq_len(length(object)),
function(i) getTrans(object[[i]], sens = sens, NAstring = NAstring, ambiguous = ambiguous, ...))
function(i) getTrans(object[[i]], sens = sens, NAstring = NAstring, ambiguous = ambiguous,
force.first.aa.to.Met = force.first.aa.to.Met, ...))

getTrans.character <- function(object, sens = "F", NAstring = "X", ambiguous = FALSE, ..., frame = 0, numcode = 1)
translate(seq = object, frame = frame, sens = sens, numcode = numcode, NAstring = NAstring, ambiguous = ambiguous)
getTrans.character <- function(object, sens = "F", NAstring = "X", ambiguous = FALSE, force.first.aa.to.Met = FALSE,
..., frame = 0, numcode = 1)
translate(seq = object, frame = frame, sens = sens, numcode = numcode, NAstring = NAstring, ambiguous = ambiguous,
force.first.aa.to.Met = force.first.aa.to.Met)

getTrans.SeqFastadna <- function(object, sens = "F", NAstring = "X", ambiguous = FALSE, ..., frame = 0, numcode = 1){
getTrans.SeqFastadna <- function(object, sens = "F", NAstring = "X", ambiguous = FALSE, force.first.aa.to.Met = FALSE,
..., frame = 0, numcode = 1){
dnaseq <- getSequence(object, as.string = FALSE)
translate(seq = dnaseq, frame = frame, sens = sens, numcode = numcode, NAstring = NAstring, ambiguous = ambiguous)
translate(seq = dnaseq, frame = frame, sens = sens, numcode = numcode, NAstring = NAstring, ambiguous = ambiguous,
force.first.aa.to.Met = force.first.aa.to.Met)
}
getTrans.SeqFrag <- getTrans.SeqFastadna

getTrans.SeqAcnucWeb <- function(object, sens = "F", NAstring = "X", ambiguous = FALSE, ..., frame = "auto", numcode = "auto"){
getTrans.SeqAcnucWeb <- function(object, sens = "F", NAstring = "X", ambiguous = FALSE, force.first.aa.to.Met = FALSE,
..., frame = "auto", numcode = "auto"){
dnaseq <- getSequence(object, as.string = FALSE)
if(numcode == "auto") numcode <- attr(object, "ncbigc")
if(frame == "auto") frame <- attr(object, "frame")
translate(seq = dnaseq, frame = frame, sens = sens, numcode = numcode, NAstring = NAstring, ambiguous = ambiguous)
translate(seq = dnaseq, frame = frame, sens = sens, numcode = numcode, NAstring = NAstring, ambiguous = ambiguous,
force.first.aa.to.Met = force.first.aa.to.Met)
}

getTrans.qaw <- function(object, sens = "F", NAstring = "X", ambiguous = FALSE, ...) getTrans(object$req, ...)
getTrans.qaw <- function(object, sens = "F", NAstring = "X", ambiguous = FALSE, force.first.aa.to.Met = FALSE, ...)
getTrans(object$req, force.first.aa.to.Met = force.first.aa.to.Met, ...)

getTrans.logical <- function (object, sens = "F", NAstring = "X", ambiguous = FALSE, ...)
getTrans.logical <- function (object, sens = "F", NAstring = "X", ambiguous = FALSE, force.first.aa.to.Met = FALSE, ...)
object # so that NA is returned for virtual lists

6 changes: 4 additions & 2 deletions R/translate.R
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@@ -1,5 +1,5 @@
translate <- function(seq, frame = 0, sens = "F", numcode = 1, NAstring = "X",
ambiguous = FALSE)
ambiguous = FALSE, force.first.aa.to.Met = FALSE)
{

if(any(seq%in%LETTERS)){
Expand Down Expand Up @@ -68,7 +68,9 @@ translate <- function(seq, frame = 0, sens = "F", numcode = 1, NAstring = "X",
if( all(allaminoacids == allaminoacids[1])) result[i] <- allaminoacids[1]
}
}

if (force.first.aa.to.Met) {
result[1] <- "M"
}
return( result )
}

19 changes: 11 additions & 8 deletions man/getTrans.Rd
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Expand Up @@ -14,14 +14,14 @@
This function translates nucleic acid sequences into the corresponding peptide sequence. It can translate in any of the 3 forward or three reverse sense frames. In the case of reverse sense, the reverse-complement of the sequence is taken. It can translate using the standard (universal) genetic code and also with non-standard codes. Ambiguous bases can also be handled.
}
\usage{
getTrans(object, sens = "F", NAstring = "X", ambiguous = FALSE, ...)
\method{getTrans}{SeqAcnucWeb}(object, sens = "F", NAstring = "X", ambiguous = FALSE, ...,
frame = "auto", numcode = "auto")
\method{getTrans}{SeqFastadna}(object, sens = "F", NAstring = "X", ambiguous = FALSE, ...,
frame = 0, numcode = 1)
\method{getTrans}{SeqFrag}(object, sens = "F", NAstring = "X", ambiguous = FALSE, ...,
frame = 0, numcode = 1)

getTrans(object, sens = "F", NAstring = "X", ambiguous = FALSE,
force.first.aa.to.Met = FALSE, ...)
\method{getTrans}{SeqAcnucWeb}(object, sens = "F", NAstring = "X", ambiguous = FALSE,
force.first.aa.to.Met = FALSE, ..., frame = "auto", numcode = "auto")
\method{getTrans}{SeqFastadna}(object, sens = "F", NAstring = "X", ambiguous = FALSE,
force.first.aa.to.Met = FALSE, ..., frame = 0, numcode = 1)
\method{getTrans}{SeqFrag}(object, sens = "F", NAstring = "X", ambiguous = FALSE,
force.first.aa.to.Met = FALSE, ..., frame = 0, numcode = 1)
}
\arguments{
\item{object}{ an object of the class \code{\link{SeqAcnucWeb}}
Expand All @@ -31,6 +31,8 @@ getTrans(object, sens = "F", NAstring = "X", ambiguous = FALSE, ...)
\item{NAstring}{ How to translate amino-acids when there are ambiguous bases in codons. }
\item{ambiguous}{ If TRUE, ambiguous bases are taken into account so that for instance
GGN is translated to Gly in the standard genetic code. }
\item{force.first.aa.to.Met}{ If TRUE, the first codon in the sequence will be translated to
Methionine regardless of the codon in order to treat rare start codons like TTG. }
\item{frame}{ Frame(s) (0,1,2) to translate. By default the frame \code{0} is used. }
\item{sens}{ Direction for translation: \code{F} for the direct strand e and \code{R} for the reverse complementary strand. }
\item{...}{further arguments passed to or from other methods}
Expand Down Expand Up @@ -82,6 +84,7 @@ getTrans(object, sens = "F", NAstring = "X", ambiguous = FALSE, ...)
#
toycds <- s2c("tctgagcaaataaatcgg")
getTrans(toycds) # should be c("S", "E", "Q", "I", "N", "R")
getTrans(toycds, force.first.aa.to.Met = TRUE) # should be c("M", "E", "Q", "I", "N", "R")
#
# Toy CDS example with ambiguous bases:
#
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7 changes: 6 additions & 1 deletion man/translate.Rd
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Expand Up @@ -10,7 +10,8 @@
be handled.
}
\usage{
translate(seq, frame = 0, sens = "F", numcode = 1, NAstring = "X", ambiguous = FALSE)
translate(seq, frame = 0, sens = "F", numcode = 1, NAstring = "X", ambiguous = FALSE,
force.first.aa.to.Met = FALSE)
}
\arguments{
\item{seq}{ the sequence to translate as a vector of single characters in lower case letters. }
Expand All @@ -20,6 +21,9 @@ translate(seq, frame = 0, sens = "F", numcode = 1, NAstring = "X", ambiguous = F
\item{NAstring}{ How to translate amino-acids when there are ambiguous bases in codons. }
\item{ambiguous}{ If TRUE, ambiguous bases are taken into account so that for instance
GGN is translated to Gly in the standard genetic code. }
\item{force.first.aa.to.Met}{ If TRUE, the first codon in the sequence will be translated to
Methionine regardless of the codon in order to treat rare start codons like TTG. }

}
\details{
The following genetic codes are described here. The number preceding each code
Expand Down Expand Up @@ -76,6 +80,7 @@ Use \code{\link{aaa}} to get the three-letter code for amino-acids.}
##
toycds <- s2c("tctgagcaaataaatcgg")
translate(seq = toycds) # should be c("S", "E", "Q", "I", "N", "R")
translate(seq = toycds, force.first.aa.to.Met = TRUE) # should be c("M", "E", "Q", "I", "N", "R")
##
## Toy CDS example with ambiguous bases:
##
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